TY - JOUR A1 - Kuzkina, A. A1 - Rößle, J. A1 - Seger, A. A1 - Panzer, C. A1 - Kohl, A. A1 - Maltese, V. A1 - Musacchio, T. A1 - Blaschke, S. J. A1 - Tamgüney, G. A1 - Kaulitz, S. A1 - Rak, K. A1 - Scherzad, A. A1 - Zimmermann, P. H. A1 - Klussmann, J. P. A1 - Hackenberg, S. A1 - Volkmann, J. A1 - Sommer, C. A1 - Sommerauer, M. A1 - Doppler, K. T1 - Combining skin and olfactory α-synuclein seed amplification assays (SAA)—towards biomarker-driven phenotyping in synucleinopathies JF - npj Parkinson’s Disease N2 - Seed amplification assays (SAA) are becoming commonly used in synucleinopathies to detect α-synuclein aggregates. Studies in Parkinson’s disease (PD) and isolated REM-sleep behavior disorder (iRBD) have shown a considerably lower sensitivity in the olfactory epithelium than in CSF or skin. To get an insight into α-synuclein (α-syn) distribution within the nervous system and reasons for low sensitivity, we compared SAA assessment of nasal brushings and skin biopsies in PD (n = 27) and iRBD patients (n = 18) and unaffected controls (n = 30). α-syn misfolding was overall found less commonly in the olfactory epithelium than in the skin, which could be partially explained by the nasal brushing matrix exerting an inhibitory effect on aggregation. Importantly, the α-syn distribution was not uniform: there was a higher deposition of misfolded α-syn across all sampled tissues in the iRBD cohort compared to PD (supporting the notion of RBD as a marker of a more malignant subtype of synucleinopathy) and in a subgroup of PD patients, misfolded α-syn was detectable only in the olfactory epithelium, suggestive of the recently proposed brain-first PD subtype. Assaying α-syn of diverse origins, such as olfactory (part of the central nervous system) and skin (peripheral nervous system), could increase diagnostic accuracy and allow better stratification of patients. KW - diagnostic markers KW - Parkinson's disease Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-357687 SN - 2373-8057 VL - 9 ER - TY - JOUR A1 - Serfling, S. A1 - Zhi, Y. A1 - Schirbel, A. A1 - Lindner, T. A1 - Meyer, T. A1 - Gerhard-Hartmann, E. A1 - Lappa, C. A1 - Hagen, R. A1 - Hackenberg, S. A1 - Buck, A. K. A1 - Scherzad, A. T1 - Improved cancer detection in Waldeyer’s tonsillar ring by \(^{68}\)Ga-FAPI PET/CT imaging JF - European Journal of Nuclear Medicine and Molecular Imaging N2 - Purpose In cancer of unknown primary (CUP), positron emission tomography/computed tomography (PET/CT) with the glucose analog [\(^{18}\)F]FDG represents the standard imaging approach for localization of the malignant primary. Frequently, however, [\(^{18}\)F]FDG PET/CT cannot precisely distinguish between small occult tumors and chronic inflammation, especially in Waldeyer’s tonsillar ring. To improve the accuracy for detecting primary tumors in the Waldeyer’s tonsillar ring, the novel PET tracer [\(^{68}\)Ga]Ga-FAPI-4 for specific imaging of fibroblast activation protein (FAP) expression was used as a more specific target for cancer imaging. Methods Eight patients with suspicion of a malignant tumor in Waldeyer’s tonsillar ring or a CUP syndrome were examined. PET/CT scans with [\(^{18}\)F]-FDG and [\(^{68}\)Ga]Ga-FAPI-4 were performed for pre-operative tumor localization. After surgical resection, histopathological and immunohistochemical results were compared to PET/CT findings. Results Histopathology revealed a palatine or lingual tonsil carcinoma in all patients. In case of lymph node metastases smaller than 7 mm in size, the [\(^{18}\)F]FDG PET/CT detection rate of cervical lymph node metastases was higher than that of [\(^{68}\)Ga]FAPI PET/CT, while both tracers identified the primary tumors in all eight cases. The size of the primary and the lymph node metastases was directly correlated to the respective FAP expression, as detected by immunohistochemistry. The mean SUVmax for the primary tumors was 21.29 ± 7.97 for \(^{18}\)F-FDG and 16.06 ± 6.29 for \(^{68}\)Ga-FAPI, respectively (p = 0.2). The mean SUVmax for the healthy contralateral tonsils was 8.38 ± 2.45 for [\(^{18}\)F]FDG and 3.55 ± 0.47 for [\(^{68}\)Ga]FAPI (p < 0.001). The SUVmax ratio of [68Ga]FAPI was significantly different from [\(^{18}\)F] FDG (p = 0.03). Mean TBRmax for the [\(^{68}\)Ga]Ga-FAPI-4 tracer was markedly higher in comparison to [\(^{18}\)F]FDG (10.90 vs. 4.11). Conclusion Non-invasive imaging of FAP expression by [\(^{68}\)Ga]FAPI PET/CT resulted in a better visual detection of the malignant primary in CUP, as compared to [\(^{18}\)F]FDG imaging. However, the detection rate of lymph node metastases was inferior, presumably due to low FAP expression in small metastases. Nevertheless, by offering a detection method for primary tumors with the potential of lower false positive rates and thus avoiding biopsies, patients with CUP syndrome may benefit from [\(^{68}\)Ga]FAPI PET/CT imaging. KW - Waldeyer’s tonsillar ring KW - cancer of unknown primary (CUP) KW - positron emission tomography/computed tomography Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-235271 SN - 1619-7070 VL - 48 ER - TY - JOUR A1 - Čuklina, Jelena A1 - Hahn, Julia A1 - Imakaev, Maxim A1 - Omasits, Ulrich A1 - Förstner, Konrad U. A1 - Ljubimov, Nikolay A1 - Goebel, Melanie A1 - Pessi, Gabriella A1 - Fischer, Hans-Martin A1 - Ahrens, Christian H. A1 - Gelfand, Mikhail S. A1 - Evguenieva-Hackenberg, Elena T1 - Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation JF - BMC Genomics N2 - Background Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters. Results A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file. Conclusions The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes. KW - Bradyrhizobium KW - RNA-seq KW - Promoter prediction KW - Genome re-annotation KW - Internal transcription start site KW - Nodule KW - Transcription start site KW - Proteogenomics KW - Antisense RNA Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-164565 VL - 17 ER - TY - JOUR A1 - Kleinsasser, N. A1 - Wiest, F. A1 - Scherzad, A. A1 - Ickrath, P. A1 - Poier, N. A1 - Hackenberg, S. T1 - Untersuchungen zum Schädigungspotenzial durch den Konsum von E-Zigaretten: In-vitro-Exposition von humanen Nasenschleimhautzellen mit Propylenglykol im Air-Liquid-Interface JF - HNO N2 - Hintergrund Die E‑Zigarette erfreut sich in den letzten Jahren zunehmender Beliebtheit. Die Frage nach der Toxizität ist jedoch noch nicht eindeutig geklärt, und es herrscht global Unsicherheit im Umgang mit der E‑Zigarette. Ziel Ziel der vorliegenden Arbeit war es, Propylenglykol, ein Hauptbestandteil der Liquide, in Bezug auf mögliche akute Entzündungsreaktionen, zyto- und genotoxische Auswirkungen auf humane Nasenschleimhautzellen zu untersuchen. Material und Methoden Die Nasenschleimhautzellen wurden von zehn Probanden im Air-Liquid-Interface kultiviert und anschließend mit unterschiedlichen Konzentrationen des Propylenglykols bedampft. Die Analyse erfolgte mittels Trypanblau-Test, Comet-Assay, Mikrokerntest und IL-6- und IL-8-Sandwich-ELISA. Ergebnis Der Trypanblau-Test zeigte keine Reduktion der Vitalität. Im Sandwich-ELISA konnte kein Anstieg der IL-6- und IL-8-Konzentrationen nachgewiesen werden. Im Comet-Assay zeigte das Olive Tail Moment eine Schädigung im Vergleich zur Negativkontrolle in allen untersuchten Konzentrationen. Zudem zeigte sich eine dosisabhängige Schädigung. Im Mikrokerntest konnte ein Unterschied zwischen dem Reinstoff und der Negativkontrolle gefunden werden. Schlussfolgerung Es zeigten sich möglicherweise reparable DNS-Schädigungen im Comet-Assay. Im Mikrokerntest konnten diese nur in der Reinstoffkonzentration bestätigt werden. Es sollte ein restriktiver Umgang mit der E‑Zigarette erfolgen, bis insbesondere Langzeitstudien vorliegen. Zudem ist eine eindeutige Deklaration der Inhaltsstoffe der Liquide durch die Hersteller zu fordern, um weitergehende Schädigungspotenziale untersuchen zu können. KW - E-Zigaretten KW - Schädigungspotenzial KW - Propylenglykol KW - Nasenschleimhautzellen Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-280329 VL - 69 ER -